Groundwater recharge plays a vital role in replenishing aquifers, which impacts on groundwater resources availability. This paper develops a geographic information system (GIS)-based water budget framework in conjunction with a hydrologic model to derive high-resolution spatial-temporal distribution of groundwater recharge for the Southern Hills aquifer system, southwestern Mississippi, and southeastern Louisiana, United States. The framework includes parallel programming to distribute the large amount of software runs to a cluster of supercomputers to expedite computation time. Under the parallel computation, the hydrologic models are calibrated by the USGS WaterWatch runoff dataset and verified by the moderate resolution imaging spectroradiometer (MODIS) evapotranspiration dataset. A map of recharge time lag is derived to understand travel time of infiltrated precipitation reaching the last soil layer. A recharge index map is derived to quantify the percentage of precipitation that becomes groundwater recharge. The results show that the mean annual recharge rate was estimated 47.5 mm/year which was 3.1% of the mean annual precipitation on the area of the Southern Hills aquifer system. High recharge rate was estimated at the outcrops of Miocene deposits in southwestern Mississippi, which are the recharge zones of the deep sands in southeastern Louisiana. This paper successfully demonstrated the applicability of the framework to groundwater recharge estimation on large-scale humid areas.